Current Computer-Aided Drug Design

Subhash C. Basak
Departments of Chemistry, Biochemistry & Molecular Biology University of Minnesota Duluth
Duluth, MN 55811
USA

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Analysis of Similarity/Dissimilarity of DNA Primary Sequences Based on Condensed Matrices and Information Entropies

Author(s): Bo Liao, Wen Zhu.

Abstract:

The primary sequence of DNA is a sequence of nucleotides over the four-letters alphabet {A, C, G, T}. Characteristic sequences of a DNA sequence are given in term of classification of bases of nucleotides. Using the characteristic sequences, we construct a set of 3 x 8 matrices and a set of 2 x 2 matrices to represent DNA primary sequences and define the information entropy, which is based on counting all triplets of characteristic sequences. Similarity and dissimilarity analysis based on the condensed matrices and the information entropies are given for the first exon of beta-globin genes sequences belonging to eleven different species.

Keywords: DNA sequence, similarity analysis, condensed matrix, information entropy

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Article Details

VOLUME: 2
ISSUE: 3
Year: 2006
Page: [275 - 285]
Pages: 11
DOI: 10.2174/157340906778226436
Price: $58